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### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:Rcollectl.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings Rcollectl_1.10.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/Rcollectl.Rcheck’
* using R version 4.5.2 (2025-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘Rcollectl/DESCRIPTION’ ... OK
* this is package ‘Rcollectl’ version ‘1.10.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘Rcollectl’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
plot_usage: no visible binding for global variable ‘tm’
plot_usage: no visible binding for global variable ‘value’
plot_usage: no visible binding for global variable ‘type’
Undefined global functions or variables:
  tm type value
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘Rcollectl-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: cl_timestamp
> ### Title: Functions to add time stamps to collectl output
> ### Aliases: cl_timestamp cl_timestamp_layer cl_timestamp_label
> 
> ### ** Examples
> 
> id <- cl_start() 
> Sys.sleep(2)
> cl_timestamp(id, "step1")
> Sys.sleep(2)
> Sys.sleep(2)
> cl_timestamp(id, "step2")
> Sys.sleep(2)
> Sys.sleep(2)
> cl_timestamp(id, "step3")
> Sys.sleep(2)
> cl_stop(id)
> path <- cl_result_path(id)
> plot_usage(cl_parse(path)) +
+   cl_timestamp_layer(path) +
+   cl_timestamp_label(path) +
+   ggplot2::theme(axis.text.x = ggplot2::element_text(angle = 90, vjust = 0.5, hjust=1))
Warning in readLines(path) : line 1 appears to contain an embedded nul
Warning in readLines(path) : line 4 appears to contain an embedded nul
Warning in readLines(path) : line 8 appears to contain an embedded nul
Warning in readLines(path) : line 9 appears to contain an embedded nul
Warning in readLines(path) : line 10 appears to contain an embedded nul
Warning in readLines(path) :
  incomplete final line found on '/tmp/Rtmp2DDgfD/file28cecb16d04cff-nebbiolo2-20251118.tab.gz'
Warning in grep("^####", full) :
  unable to translate '<8b>' to a wide string
Warning in grep("^####", full) : input string 1 is invalid
Warning in grep("^####", full) :
  unable to translate '<93><fa><80><e3>4<ec><d3>Ք<b1><cb>2kn<97><f5>"<ee>w<92>5ygm <84><c0>N9<e9><9b><e6>3:<b6><b3>J۠<b5>gW<bf><e3><e4><dc>p<8e><95><d3><cd><cd><f4><fb>:<ad><8d>,<b6>l؇<aa><c9>뇬$d<9b><c5><f1><e5><f4>:ɾ<9e><fd><eb><f2>trM}G<92><b3><f7>ev<87><b1><...' to a wide string
Warning in grep("^####", full) : input string 2 is invalid
Warning in grep("^####", full) :
  unable to translate '?<e6>u<95><97>I<a7>=<f0>|<e4><c2><e8>.<af><f2><ba><98>1v<8e>ˮ<bf>C<83><da>r<85><a5><f7>G<d0><f5><df>l<85><d5><8auA<e1>n<ef>#I<d7>|<91>-h<93><f5><<c3><ef>M<9a>r<91>7<89>lțvF<b9><ff><fc>3˫h<cd>oy<b5><e2><83>
ad<80><96>WK<91>Ɩ<92><fe>ϗ<b...' to a wide string
Warning in grep("^####", full) : input string 3 is invalid
Warning in grep("^####", full) :
  unable to translate '9'1&<97><8e><a1><88><9c><c1>+<f3>#rnHN<af><b5>9n<82><e8><c8><e1>T g $rA<c7>~<85><a6><94>Z<e2><93><c8>I<e1><f7>$<a7><94>3<b2>#g<bd>ĥAW <9c>7' to a wide string
Warning in grep("^####", full) : input string 4 is invalid
Warning in grep("^####", full) :
  unable to translate '<eb><fc><b3><88><d1>3(\i<a5>ۨFʼn<e2>8<9b><c0><c9>8<93>|G@̑F<bf>Ӝ^<c2>f<f6><f0>8Xa)mY|<84>T<c9>#v<e4><b4><f1><ed>K<a1>(Z5<f4>c<be>s"^X<b3><df>>g<f1><fa>o<b1><a3>h<85><a6><e4>G΃W<e9>~<e0>p' to a wide string
Warning in grep("^####", full) : input string 5 is invalid
Warning in grep("^####", full) :
  unable to translate 'ބ<c2>e~d<8f>XS<a8><d1>%<b4>' to a wide string
Warning in grep("^####", full) :
  unable to translate ',<d1>J<be><e0>r<b6>Gr<dd>' to a wide string
Warning in grep("^####", full) :
  unable to translate 'P<b0><b7>.<e7>]' to a wide string
Warning in grep("^####", full) :
  unable to translate '3<90><8f><c9>ZM<8f><eb><c1>U<e1>Y*F$s<a0><87><fb>I<a5>T<88>	<e4>v<80><a2><87>BK<fa><9c>'l<b7><88>&<fa>}ҿ<92><f4>4<d5>cH<9f><e4>v*<ba>`W<e6>=<9e><b8><a0>2*P<a9><80><<d4>&<f4>$nE<e9>䂖<f4><c1>ϩړB;xGD<f0>f<ca>}Ar<b9>+<f3>$j<c6><b3><94>g<9...' to a wide string
Warning in grep("^####", full) :
  unable to translate '<af><a0><bd><9e><c3>S<fc>	<<c4>"<f2>'<e0><e7>R1x<c1>Ex!<b9><e0><f9>X,<9a>' to a wide string
Error in cl_parse(path) : length(inds) == 2 is not TRUE
Calls: plot_usage ... cpu_active -> data.frame -> as.POSIXct -> cl_parse -> stopifnot
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
cl_result_path 0.585  0.246   6.316
cl_start       0.548  0.236   6.281
cl_stop        0.568  0.199   6.289
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/Rcollectl.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL Rcollectl
###
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* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘Rcollectl’ ...
** this is package ‘Rcollectl’ version ‘1.10.0’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (Rcollectl)

R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(Rcollectl)
> 
> test_check("Rcollectl")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 8 ]
> 
> proc.time()
   user  system elapsed 
  5.564   0.636  15.642